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Magnesium deficiency (MGD) is particularly prominent in tropical and subtropical regions where sugarcane is grown, but the response mechanism to MGD in sugarcane remains unknown. Physiological and transcriptomic analysis of the three founding Saccharum species under different magnesium (Mg) levels was performed. Our result showed that MGD decreased chlorophyll content and photosynthetic efficiency of three Saccharum species but led to increased starch in leaves and lignin content in roots of Saccharum robustum and Saccharum spontaneum. We identified 12,129, 11,306 and 12,178 differentially expressed genes (DEGs) of Saccharum officinarum, Saccharum robustum and Saccharum spontaneum, respectively. In Saccharum officinarum, MGD affected signal transduction by up-regulating the expression of xylan biosynthesis process-related genes. Saccharum robustum, responded to the MGD by regulating the expression of transcription and detoxification process-related genes. Saccharum spontaneum, avoids damage from MGD by regulating the expression of the signing transduction process and the transformation from growth and development to reproductive development. This novel repertoire of candidate genes related to MGD response in sugarcane will be helpful for engineering MGD tolerant varieties.<\/jats:p>","DOI":"10.3390\/ijms23179681","type":"journal-article","created":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T01:39:19Z","timestamp":1661737159000},"page":"9681","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Transcriptome Dynamics Underlying Magnesium Deficiency Stress in Three Founding Saccharum Species"],"prefix":"10.3390","volume":"23","author":[{"given":"Yongjun","family":"Wang","sequence":"first","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yihan","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuting","family":"Hua","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianqu","family":"Fan","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9919-1940","authenticated-orcid":false,"given":"Wei","family":"Yao","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3138-3422","authenticated-orcid":false,"given":"Muqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jisen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China"},{"name":"Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1590\/S1516-89132013000500004","article-title":"Photosynthetic capacity and water use efficiency in sugarcane genotypes subject to water deficit during early growth phase","volume":"56","author":"Silva","year":"2013","journal-title":"Braz. 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